Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts.
The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224).
This application is developed based on this thesis "Iterative reconstruction of three-dimensional model of human chromosomes from chromosomal contact data". (Ready for publication)
- Use chromosomal contact data acquired using the Hi-C technique
- Construct 3D structural genome and chromosome models from chromosomal contact data
- Initialize the coordinates using probabilistic approach
- Novel method to represent satisfied contacts in heat map matrix
- Scoring schemes to figure out long range and short range contacts
- Compared with other existing method and also validated with genome features
Be the first to post a review of Gen3D!